Conserved genomic landscapes of differentiation across Populus speciation continuum

Investigating genome-wide variation patterns along a speciation continuum is of central importance to understand the evolutionary processes contributing to lineage diversification. To identify which forces have shaped the genomic landscapes in Populus, we resequenced 201 individuals from eight closely related species, with pairs of species at different stages along the speciation continuum. Using population structure and identity by descent analyses, we show extensive introgression between some species pairs, especially those with parapatric distributions. Inference of historical changes in effective population sizes support species-specific demographic trajectories, including recent population expansions in species characterized by broad present-day distributions. We observed highly conserved genomic landscapes, either focusing on within-species (genetic diversity and recombination rate) or among-species variation (relative and absolute divergence levels). Independent of the stage across the divergence continuum, we recovered negative correlations between nucleotide diversity and relative divergence across all species pairs, which is consistent with a substantial contribution of linked selection in shaping these genomic landscapes. However, the positive correlations between nucleotide diversity and absolute divergence landscapes became weaker as the overall divergence level (da) increased, suggesting that background selection is not the only factor at play. Negative correlations between introgression (fd) and FST in some species pairs suggest an additional role of gene flow in shaping genomic landscapes of differentiation.Nevertheless, linked selection and recombination rate variation predominantly shape the heterogeneous genomic landscape of divergence in Populus.